Computational diagnostic methods for identifying organisms and applications thereof

Abstract

Methods for identifying organisms within a mixture using a minimal set of reagents are provided. The methods also allow for identifying the presence of not yet sequenced organisms, as well as for classification based on evolutionary lineage.

1 . A method for generating a decision path for determining the presence of an organism in a sample, comprising:
 (a) providing two or more organism information sequences;   (b) aligning the two or more organism information sequences;   (c) determining one or more common regions of the organism information sequences; and   (d) determining a number of probes required to identify the one or more organism information sequences, thereby determining one or more decision paths for determining the presence of an organism.   
     
     
         2 . The method of  claim 1 , wherein (a) comprises providing nucleic acid and/or amino acid organism information sequences. 
     
     
         3 . The method of  claim 2 , wherein (a) comprises providing eukaryotic or prokaryotic sequences, or a mixture thereof. 
     
     
         4 . A method for identifying an organism, comprising:
 (a) providing a plurality of organisms;   (b) providing one or more organism information sequences of the organisms;   (c) applying a first set of probes to the organism information sequences;   (d) determining the presence of a target organism information sequence, wherein an interaction between one or more probes of the first set and a first target organism information sequence indicates the presence of the first organism information sequence;   (e) applying a decision path to determine a subsequent set of probes to be applied;   (f) applying the subsequent set of probes to the organism information sequences, wherein an interaction between one or more probes of the subsequent set and a second target organism information sequence indicates the presence of the second target organism information sequence; and   (g) repeating (e)-(f) one or more times, wherein a final interaction between one or more probes and a final target organism information sequence identifies the organism.   
     
     
         5 . The method of  claim 4 , wherein (b) comprises providing nucleic acid and/or amino acid organism information sequences. 
     
     
         6 . The method of  claim 5 , wherein (b) comprises providing eukaryotic or prokaryotic sequences, or a mixture thereof. 
     
     
         7 . A decision path for determining the presence of an organism in a sample, the decision path generated by a method comprising:
 (a) providing two or more organism information sequences;   (b) aligning the two or more organism information sequences;   (c) determining one or more common regions of the organism information sequences; and   (d) determining a number of probes required to identify the one or more organism information sequences, thereby generating one or more decision paths for determining the presence of an organism.   
     
     
         8 . The decision path of  claim 7 , wherein (a) comprises providing nucleic acid and/or amino acid organism information sequences. 
     
     
         9 . The decision path of  claim 8 , wherein (a) comprises providing eukaryotic or prokaryotic sequences, or a mixture thereof.